Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.GMO.cell.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.001299/0.001299, allocations: 92.2 kB / 20.19 MB, free: 4.363 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.0009553/0.0009553, allocations: 173 kB / 23.49 MB, free: 1.062 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 1.02/1.02, allocations: 177.1 MB / 203.8 MB, free: 5.652 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo): time 0.06558/0.06558, allocations: 9.547 MB / 269.8 MB, free: 4.023 MB / 250.7 MB
"
[Timeout remaining time 180]
Using package BioChem with version 1.1.3 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell")
translateModel(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.332e-06/1.332e-06, allocations: 0 / 342.9 MB, free: 7.086 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.982e-05/2.115e-05, allocations: 2.312 kB / 342.9 MB, free: 7.082 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005079/0.0051, allocations: 4.502 MB / 347.4 MB, free: 2.562 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0003862/0.005486, allocations: 299.3 kB / 347.7 MB, free: 2.27 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001161/0.005602, allocations: 16 kB / 347.7 MB, free: 2.254 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 9.457e-05/0.005697, allocations: 51.55 kB / 347.8 MB, free: 2.203 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001779/0.005875, allocations: 75.17 kB / 347.8 MB, free: 2.129 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001843/0.006059, allocations: 75.86 kB / 347.9 MB, free: 2.055 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0002407/0.0063, allocations: 311.1 kB / 348.2 MB, free: 1.746 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002127/0.006512, allocations: 109 kB / 348.3 MB, free: 1.641 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001558/0.006668, allocations: 199.6 kB / 348.5 MB, free: 1.445 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001978/0.006866, allocations: 115.6 kB / 348.6 MB, free: 1.332 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 6.774e-05/0.006934, allocations: 32 kB / 348.7 MB, free: 1.301 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.646e-05/0.00696, allocations: 32 kB / 348.7 MB, free: 1.27 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 3.047e-05/0.006991, allocations: 71.75 kB / 348.8 MB, free: 1.199 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 6.676e-05/0.007057, allocations: 115.7 kB / 348.9 MB, free: 1.086 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0001889/0.007246, allocations: 235.1 kB / 349.1 MB, free: 0.8555 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.226e-06/0.007249, allocations: 3.984 kB / 349.1 MB, free: 0.8516 MB / 266.7 MB
Notification: Performance of FrontEnd: time 1.232e-06/0.007251, allocations: 4 kB / 349.1 MB, free: 0.8477 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 4.147e-06/0.007255, allocations: 0 / 349.1 MB, free: 0.8477 MB / 266.7 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 96
 * Number of variables: 96
Notification: Performance of Generate backend data structure: time 0.0004713/0.007726, allocations: 0.6291 MB / 349.7 MB, free: 180 kB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 2.747e-05/0.007753, allocations: 12.03 kB / 349.7 MB, free: 168 kB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.83e-05/0.007812, allocations: 68.7 kB / 349.8 MB, free: 100 kB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 9.164e-05/0.007903, allocations: 148.1 kB / 350 MB, free: 15.93 MB / 282.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.16e-05/0.007925, allocations: 33.36 kB / 350 MB, free: 15.89 MB / 282.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.953e-05/0.007965, allocations: 36.38 kB / 350 MB, free: 15.86 MB / 282.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002603/0.008225, allocations: 247.1 kB / 350.3 MB, free: 15.61 MB / 282.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.163e-05/0.008237, allocations: 192 / 350.3 MB, free: 15.61 MB / 282.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.05e-05/0.008257, allocations: 16.38 kB / 350.3 MB, free: 15.59 MB / 282.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.317e-06/0.008266, allocations: 8.375 kB / 350.3 MB, free: 15.59 MB / 282.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001895/0.008456, allocations: 149.8 kB / 350.4 MB, free: 15.44 MB / 282.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001042/0.009498, allocations: 0.9251 MB / 351.4 MB, free: 14.48 MB / 282.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000196/0.009694, allocations: 154.9 kB / 351.5 MB, free: 14.32 MB / 282.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 9.936e-05/0.009793, allocations: 91.48 kB / 351.6 MB, free: 14.23 MB / 282.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 9.498e-06/0.009803, allocations: 4 kB / 351.6 MB, free: 14.22 MB / 282.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.956e-05/0.009822, allocations: 41.38 kB / 351.7 MB, free: 14.17 MB / 282.7 MB
Notification: Performance of pre-optimization done (n=22): time 1.212e-06/0.009823, allocations: 0 / 351.7 MB, free: 14.17 MB / 282.7 MB
Notification: Performance of matching and sorting (n=26): time 0.0009757/0.0108, allocations: 0.708 MB / 352.4 MB, free: 13.43 MB / 282.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.104e-05/0.01083, allocations: 59.41 kB / 352.4 MB, free: 13.36 MB / 282.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001085/0.01094, allocations: 230.4 kB / 352.6 MB, free: 13.11 MB / 282.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.484e-05/0.01095, allocations: 33.7 kB / 352.7 MB, free: 13.07 MB / 282.7 MB
Notification: Performance of collectInitialEqns (initialization): time 8.517e-05/0.01104, allocations: 254.8 kB / 352.9 MB, free: 12.82 MB / 282.7 MB
Notification: Performance of collectInitialBindings (initialization): time 5.045e-05/0.01109, allocations: 107.1 kB / 353 MB, free: 12.71 MB / 282.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.998e-05/0.01115, allocations: 71.34 kB / 353.1 MB, free: 12.64 MB / 282.7 MB
Notification: Performance of setup shared object (initialization): time 0.0002293/0.01138, allocations: 0.4962 MB / 353.6 MB, free: 12.13 MB / 282.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.05e-05/0.01145, allocations: 56.34 kB / 353.6 MB, free: 12.07 MB / 282.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001642/0.01161, allocations: 223.3 kB / 353.9 MB, free: 11.79 MB / 282.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003003/0.01191, allocations: 367.4 kB / 354.2 MB, free: 11.36 MB / 282.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.533e-06/0.01191, allocations: 4 kB / 354.2 MB, free: 11.36 MB / 282.7 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0002931/0.01221, allocations: 305.1 kB / 354.5 MB, free: 11.05 MB / 282.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.226e-05/0.01222, allocations: 11.94 kB / 354.5 MB, free: 11.04 MB / 282.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.44e-06/0.01223, allocations: 4 kB / 354.5 MB, free: 11.04 MB / 282.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.242e-05/0.01224, allocations: 4 kB / 354.5 MB, free: 11.03 MB / 282.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002971/0.01254, allocations: 79.91 kB / 354.6 MB, free: 10.95 MB / 282.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.745e-06/0.01254, allocations: 11.92 kB / 354.6 MB, free: 10.94 MB / 282.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.322e-05/0.01262, allocations: 12.47 kB / 354.6 MB, free: 10.93 MB / 282.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.85e-05/0.01263, allocations: 16 kB / 354.7 MB, free: 10.91 MB / 282.7 MB
Warning: Assuming fixed start value for the following 5 variables:
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         ambientSubstance.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         X.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         M.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         C.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 16
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (46):
 * Single equations (assignments): 46
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0001494/0.01278, allocations: 190.4 kB / 354.9 MB, free: 10.71 MB / 282.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.558e-05/0.01282, allocations: 35.8 kB / 354.9 MB, free: 10.68 MB / 282.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.023e-05/0.01286, allocations: 37.91 kB / 354.9 MB, free: 10.64 MB / 282.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.774e-06/0.01286, allocations: 0 / 354.9 MB, free: 10.64 MB / 282.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.816e-06/0.01286, allocations: 0 / 354.9 MB, free: 10.64 MB / 282.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.388e-06/0.01287, allocations: 7.922 kB / 354.9 MB, free: 10.63 MB / 282.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0002292/0.0131, allocations: 252.5 kB / 355.2 MB, free: 10.35 MB / 282.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.173e-06/0.0131, allocations: 0 / 355.2 MB, free: 10.35 MB / 282.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001365/0.01324, allocations: 43.97 kB / 355.2 MB, free: 10.31 MB / 282.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.485e-06/0.01324, allocations: 3.984 kB / 355.2 MB, free: 10.3 MB / 282.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.473e-05/0.01325, allocations: 11.94 kB / 355.2 MB, free: 10.29 MB / 282.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.092e-06/0.01325, allocations: 0 / 355.2 MB, free: 10.29 MB / 282.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.202e-06/0.01326, allocations: 0 / 355.2 MB, free: 10.29 MB / 282.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003432/0.0136, allocations: 423.6 kB / 355.6 MB, free: 9.859 MB / 282.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.442e-05/0.01361, allocations: 19.91 kB / 355.7 MB, free: 9.84 MB / 282.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 1.985e-05/0.01363, allocations: 7.938 kB / 355.7 MB, free: 9.832 MB / 282.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.35e-05/0.0137, allocations: 4 kB / 355.7 MB, free: 9.828 MB / 282.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.669e-05/0.01372, allocations: 19.95 kB / 355.7 MB, free: 9.809 MB / 282.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.264e-06/0.01373, allocations: 4 kB / 355.7 MB, free: 9.805 MB / 282.7 MB
Notification: Performance of sorting global known variables: time 5.396e-05/0.01378, allocations: 155.9 kB / 355.9 MB, free: 9.652 MB / 282.7 MB
Notification: Performance of sort global known variables: time 6e-08/0.01378, allocations: 0 / 355.9 MB, free: 9.652 MB / 282.7 MB
Notification: Performance of remove unused functions: time 0.0001991/0.01398, allocations: 64 kB / 355.9 MB, free: 9.59 MB / 282.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,C.n,M.n,X.n,ambientSubstance.n)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (26):
 * Single equations (assignments): 26
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 7.296e-05/0.01406, allocations: 103.2 kB / 356 MB, free: 9.48 MB / 282.7 MB
Notification: Performance of simCode: created initialization part: time 0.0002181/0.01427, allocations: 199.3 kB / 356.2 MB, free: 9.281 MB / 282.7 MB
Notification: Performance of simCode: created event and clocks part: time 8.72e-07/0.01428, allocations: 0 / 356.2 MB, free: 9.281 MB / 282.7 MB
Notification: Performance of simCode: created simulation system equations: time 8.358e-05/0.01436, allocations: 91.58 kB / 356.3 MB, free: 9.188 MB / 282.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0001915/0.01455, allocations: 24.92 kB / 356.3 MB, free: 9.164 MB / 282.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0009028/0.01545, allocations: 0.6476 MB / 357 MB, free: 8.488 MB / 282.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.753e-05/0.0155, allocations: 88.31 kB / 357.1 MB, free: 8.383 MB / 282.7 MB
Notification: Performance of simCode: alias equations: time 6.213e-05/0.01556, allocations: 25.94 kB / 357.1 MB, free: 8.355 MB / 282.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.734e-05/0.01561, allocations: 20.5 kB / 357.1 MB, free: 8.336 MB / 282.7 MB
Notification: Performance of SimCode: time 5.31e-07/0.01561, allocations: 0 / 357.1 MB, free: 8.336 MB / 282.7 MB
Notification: Performance of Templates: time 0.003548/0.01916, allocations: 2.014 MB / 359.1 MB, free: 6.355 MB / 282.7 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.GMO.cell.makefile [Timeout 660]
(rm -f BioChem_BioChem.Examples.GMO.cell.pipe ; mkfifo BioChem_BioChem.Examples.GMO.cell.pipe ; head -c 1048576 < BioChem_BioChem.Examples.GMO.cell.pipe >> ../files/BioChem_BioChem.Examples.GMO.cell.sim & ./BioChem_BioChem.Examples.GMO.cell -abortSlowSimulation -alarm=240  -lv LOG_STATS > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 2.949499584035948]